Variant report

Variant	rs61959992
Chromosome Location	chr13:50020280-50020281
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr13:50019913-50020307	K562	blood:	n/a	n/a
2	POLR2A	chr13:50017428-50020327	HL-60	blood:	n/a	n/a
3	MYC	chr13:50020021-50020291	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:49820702..49823407-chr13:50017509..50020339,3	MCF-7	breast:
2	chr13:50016715..50020360-chr13:50068508..50074036,7	MCF-7	breast:
3	chr13:49820441..49822930-chr13:50018500..50020473,2	K562	blood:
4	chr13:50016483..50020444-chr13:50068529..50072853,4	MCF-7	breast:
5	chr13:50020071..50022197-chr13:50067941..50070115,2	K562	blood:

No data

Variant related genes	Relation type
CAB39L	TF binding region
ENSG00000136147	Chromatin interaction
ENSG00000102543	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11619265	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12429813	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1322787	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1358991	0.87[ASN][1000 genomes]
rs1409017	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1543513	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038638	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2057414	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2057416	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2077848	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2407691	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35980977	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764089	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4941643	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942830	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6561526	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs721457	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7317772	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7326345	0.81[ASN][1000 genomes]
rs7327520	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7987940	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7991226	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7995283	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7997737	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9316454	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526563	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535244	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535247	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535251	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv1807924	chr13:49991885-50036730	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1796315	chr13:49992988-50031868	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61959992	PHF11	Cis_1M	lymphoblastoid	RTeQTL
rs61959992	CAB39L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50017000-50022000	Active TSS	NHLF	lung
2	chr13:50017200-50020800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr13:50017200-50022200	Active TSS	K562	blood
4	chr13:50017200-50022400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:50017400-50020800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:50019000-50021200	Flanking Active TSS	Dnd41	blood
7	chr13:50019400-50021400	Active TSS	HepG2	liver
8	chr13:50019400-50036200	Weak transcription	Esophagus	oesophagus
9	chr13:50019600-50020600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:50019600-50022200	Weak transcription	Ovary	ovary
11	chr13:50019600-50022400	Enhancers	Fetal Heart	heart
12	chr13:50019600-50024200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:50019600-50028200	Weak transcription	Fetal Stomach	stomach
14	chr13:50019600-50028600	Weak transcription	Fetal Lung	lung
15	chr13:50019600-50034400	Weak transcription	Adipose Nuclei	Adipose
16	chr13:50019600-50035400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr13:50019600-50035400	Weak transcription	Brain Substantia Nigra	brain
18	chr13:50019600-50035800	Weak transcription	Left Ventricle	heart
19	chr13:50019600-50035800	Weak transcription	HSMM	muscle
20	chr13:50019600-50036000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:50019800-50020400	Enhancers	Primary B cells from cord blood	blood
22	chr13:50019800-50020400	Weak transcription	Brain Angular Gyrus	brain
23	chr13:50019800-50020400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr13:50019800-50020600	Enhancers	Primary B cells from peripheral blood	blood
25	chr13:50019800-50020600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr13:50019800-50020600	Weak transcription	Colon Smooth Muscle	Colon
27	chr13:50019800-50020600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr13:50019800-50020600	Enhancers	Thymus	Thymus
29	chr13:50019800-50020800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr13:50019800-50020800	Weak transcription	Brain Anterior Caudate	brain
31	chr13:50019800-50020800	Weak transcription	Brain Hippocampus Middle	brain
32	chr13:50019800-50020800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr13:50019800-50021000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:50019800-50021000	Enhancers	Fetal Intestine Small	intestine
35	chr13:50019800-50021000	Weak transcription	Osteobl	bone
36	chr13:50019800-50021200	Enhancers	Liver	Liver
37	chr13:50019800-50021400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:50019800-50021600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:50019800-50021600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr13:50019800-50021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr13:50019800-50022000	Enhancers	Primary hematopoietic stem cells	blood
42	chr13:50019800-50022000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr13:50019800-50022800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr13:50019800-50023200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr13:50019800-50023200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr13:50019800-50023400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr13:50019800-50028400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:50019800-50028600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr13:50019800-50035200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr13:50019800-50035200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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